Changeset 960 for trunk/src

Timestamp:

Jun 25, 2016, 11:20:40 AM (9 years ago)

Author:

sommeria

Message:

aver_stat modified to deal with volume slices

Location:

trunk/src/series

Files:

• aver_stat.m (modified) (13 diffs)
• merge_proj.m (modified) (2 diffs)
• time_series.m (modified) (1 diff)

trunk/src/series/aver_stat.m

@@ -14 +14 @@
 % in series), the function ouput paramOut set the activation of the needed GUI elements
 %
-% Param contains the elements:(use the menu bar command 'export/GUI config' in series to 
+% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
 % see the current structure Param)
 %    .InputTable: cell of input file names, (several lines for multiple input)
@@ -25 +25 @@
 %             .RUN =0 for GUI input, =1 for function activation
 %             .RunMode='local','background', 'cluster': type of function  use
-%             
+%
 %    .IndexRange: set the file or frame indices on which the action must be performed
 %    .FieldTransform: .TransformName: name of the selected transform function
@@ -70 +70 @@
     ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
     ParamOut.OutputDirExt='.stat';%set the output dir extension
-    ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
-     % check for selection of a projection object
+    ParamOut.OutputFileMode='NbSlice';% '=NbInput': one output file per input file index, '=NbInput_i': one file per input file index i, '=NbSlice': one file per slice
+    % check for selection of a projection object
     hseries=findobj(allchild(0),'Tag','series');% handles of the GUI series
     if  ~isfield(Param,'ProjObject')
@@ -106 +106 @@
         [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
         LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
-        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
+            Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
         if ~exist(LastFileName,'file')
-             msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist'])
+            msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist'])
         end
     end
     % determine volume scan mode
-        prompt = {'volume scan mode (Yes/No)'};
+    prompt = {'volume scan mode (Yes/No)'};
     dlg_title = 'determine volume scan';
     num_lines= 1;
     def     = { 'No'};
-     answer=msgbox_uvmat('INPUT_Y-N','volume scan mode (OK/No)?');
-%     answer = inputdlg(prompt,dlg_title,num_lines,def);
+    answer=msgbox_uvmat('INPUT_Y-N','volume scan mode (OK/No)?');
+    %     answer = inputdlg(prompt,dlg_title,num_lines,def);
     if isempty(answer)
         return
     end
     %check input consistency
-    if strcmp(answer,'Yes') 
-            ParamOut.NbSlice=1;% set NbSlice to 1 ( for i index)
-            ParamOut.ActionInput.CheckVolume=1;
+    if strcmp(answer,'Yes')
+        ParamOut.NbSlice=1;% set NbSlice to 1 ( for i index)
+        ParamOut.ActionInput.CheckVolume=1;
     end
     return
@@ -143 +143 @@
 %% define the directory for result file (with path=RootPath{1})
 OutputDir=[Param.OutputSubDir Param.OutputDirExt];
-    
+
 %% root input file(s) name, type and index series
 RootPath=Param.InputTable(:,1);
@@ -150 +150 @@
 NomType=Param.InputTable(:,4);
 FileExt=Param.InputTable(:,5);
+
 hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
+% gives the series of input file names and indices set by the input parameters:
 [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
-if ~isempty(hdisp),delete(hdisp),end;
-%%%%%%%%%%%%
-% The cell array filecell is the list of input file names, while
 % filecell{iview,fileindex}:
 %        iview: line in the table corresponding to a given file series
-%        fileindex: file index within  the file series, 
-% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j 
+%        fileindex: file index with i and j reshaped as a 1D array
+% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j
 % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
-%%%%%%%%%%%%
+if ~isempty(hdisp),delete(hdisp),end;%end the waiting display
+
 NbView=numel(i1_series);%number of input file series (lines in InputTable)
 NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
@@ -166 +166 @@
 NbField=NbField_j*NbField_i; %total number of fields
 
-%% determine the file type on each line from the first input file 
+%% determine the file type on each line from the first input file
 ImageTypeOptions={'image','multimage','mmreader','video'};
 NcTypeOptions={'netcdf','civx','civdata'};
@@ -191 +191 @@
     if diff_time>0
         disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
-    end   
+    end
 end
 
@@ -201 +201 @@
     rmpath(Param.FieldTransform.TransformPath)
     if isfield(Param,'TransformInput')
-            XmlData{1}.TransformInput=Param.TransformInput;
-    end     
+        XmlData{1}.TransformInput=Param.TransformInput;
+    end
 end
 
 %%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
- % EDIT FROM HERE
+% EDIT FROM HERE
 
 %% check the validity of  input file types and set the output file type
@@ -222 +222 @@
 end
 if isfield(Param,'ProjObject') && ~strcmp(Param.ProjObject.Type,'plane')
-      FileExtOut='.nc';% write result as .nc files (even for image input)
+    FileExtOut='.nc';% write result as .nc files (even for image input)
 end
 
@@ -253 +253 @@
     end
 end
-nbfiles=0;%counter of the successfully read files (bad files are skipped)
+
 VarMesh=[];
 if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})
-    if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'VarMesh')%case of histograms 
-     VarMesh=Param.ActionInput.VarMesh;
+    if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'VarMesh')%case of histograms
+        VarMesh=Param.ActionInput.VarMesh;
     else
-       VarMesh=[];
-       disp_uvmat('WARNING','automatic bin size for histograms, select aver_stat again to set the value',checkrun)
-    end
-end
-
-%% set volume scan
-NbSlice_j=1;
+        VarMesh=[];
+        disp_uvmat('WARNING','automatic bin size for histograms, select aver_stat again to set the value',checkrun)
+    end
+end
+
+NbSlice_j=1;% number of j slices =1 except fo volume scan
 index_series=1:size(filecell,2);
-first_j_out=first_j;
-last_j_out=last_j;
+index_j=1;
+
+%% set volume scan if requested
+first_j_out=first_j;%first j index to use  for the output file name
+last_j_out=last_j;%last j index to use for the output file name
 if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'CheckVolume') ...
         && Param.ActionInput.CheckVolume
-   index_j=Param.IndexRange.first_j:Param.IndexRange.incr_j:Param.IndexRange.last_j;
-   NbSlice_j=numel(index_j);
-   index_i=index_series(1:NbSlice_j:end);
-end
-
-%%% loop on slices (volume scan)
+    index_j=Param.IndexRange.first_j:Param.IndexRange.incr_j:Param.IndexRange.last_j;
+    NbSlice_j=numel(index_j);
+    index_series=1:NbSlice_j:size(filecell,2);
+end
+
+%% loop on j slices (volume scan)
 for islice=index_j
+    nbfiles=0;%counter of the successfully read files (bad files are skipped)
     if NbSlice_j>1
-    first_j_out=islice;
-    last_j_out=islice;
-    
+        first_j_out=islice;%first and last  j index to use  for the output file name are the current j index
+        last_j_out=islice;
     end
     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
-    for index=index_i+index_j(islice)
+    for index=index_series+index_j(islice)-index_j(1)
         update_waitbar(WaitbarHandle,index/NbField)
         if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
@@ -295 +297 @@
         for iview=1:NbView
             % reading input file(s)
-            %InputFile=fullfile_uvmat(RootPath{iview},SubDir{iview},RootFile{iview},FileExt{iview},NomType{iview},first_i,last_i,first_j_out,last_j_out);
             [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
             if ~isempty(errormsg)
                 errormsg=['error of input reading: ' errormsg];
-                break
+                break% leave the loop on views in case of error
             end
             if ~isempty(NbSlice_calib)
@@ -307 +308 @@
         %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%%
         
-        if isempty(errormsg)
-            Field=Data{1}; % default input field structure
-            nbfiles=nbfiles+1; %increment the file counter
-            %% coordinate transform (or other user defined transform)
-            if ~isempty(transform_fct)
-                switch nargin(transform_fct)
-                    case 4
-                        if length(Data)==2
-                            Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
-                        else
-                            Field=transform_fct(Data{1},XmlData{1});
-                        end
-                    case 3
-                        if length(Data)==2
-                            Field=transform_fct(Data{1},XmlData{1},Data{2});
-                        else
-                            Field=transform_fct(Data{1},XmlData{1});
-                        end
-                    case 2
+        if ~isempty(errormsg)
+            disp(errormsg)
+            continue % go to next input field in case of error (file skipped in the average)
+        end
+        Field=Data{1}; % default input field structure
+        nbfiles=nbfiles+1; %increment the file counter
+        
+        %% coordinate transform (or other user defined transform)
+        if ~isempty(transform_fct)
+            switch nargin(transform_fct)
+                case 4
+                    if length(Data)==2
+                        Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
+                    else
                         Field=transform_fct(Data{1},XmlData{1});
-                    case 1
-                        Field=transform_fct(Data{1});
+                    end
+                case 3
+                    if length(Data)==2
+                        Field=transform_fct(Data{1},XmlData{1},Data{2});
+                    else
+                        Field=transform_fct(Data{1},XmlData{1});
+                    end
+                case 2
+                    Field=transform_fct(Data{1},XmlData{1});
+                case 1
+                    Field=transform_fct(Data{1});
+            end
+        end
+        
+        %% field projection on an object
+        if Param.CheckObject
+            if strcmp(Param.ProjObject.ProjMode,'interp_tps')
+                Field=tps_coeff_field(Field,check_proj_tps);% calculate tps coefficients if needed
+            end
+            [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh);
+            if ~isempty(errormsg)
+                disp_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg],checkrun)
+                return
+            end
+        end
+        
+        %%%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
+        if nbfiles==1 %first field
+            time_1=[];
+            if isfield(Field,'Time')
+                time_1=Field.Time(1);
+            end
+            DataOut=Field;%outcome reproduces the first (projected) field by default
+            DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files
+            if isfield(Param,'ProjObject')&& ismember(Param.ProjObject.ProjMode,{'inside','outside'})%case of histograms
+                for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram)
+                    VarName=Field.ListVarName{ivar};
+                    if isfield(Data{1},VarName)
+                        DataOut.(VarName)=Field.(VarName);
+                        DataOut.([VarName 'Histo'])=zeros(size(DataOut.(VarName)));
+                        VarMesh=DataOut.(VarName)(2)-DataOut.(VarName)(1);
+                    end
                 end
-            end
-            
-            %% field projection on an object
-            if Param.CheckObject
-                if strcmp(Param.ProjObject.ProjMode,'interp_tps')
-                    Field=tps_coeff_field(Field,check_proj_tps);% calculate tps coefficients if needed
-                end
-                [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh);
-                if ~isempty(errormsg)
-                    disp_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg],checkrun)
-                    return
-                end
-            end
-            
-            %%%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
-            if nbfiles==1 %first field
-                time_1=[];
-                if isfield(Field,'Time')
-                    time_1=Field.Time(1);
-                end
-                DataOut=Field;%outcome reproduces the first (projected) field by default
-                DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files
-                if isfield(Param,'ProjObject')&& ismember(Param.ProjObject.ProjMode,{'inside','outside'})%case of histograms
-                    for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram)
+                disp(['mesh for histogram = ' num2str(VarMesh)])
+            else
+                errorvar=zeros(numel(Field.ListVarName));%index of errorflag associated to each variable
+                if isfield(Field,'VarAttribute')
+                    for ivar=1:numel(Field.ListVarName)
                         VarName=Field.ListVarName{ivar};
-                        if isfield(Data{1},VarName)
-                            DataOut.(VarName)=Field.(VarName);
-                            DataOut.([VarName 'Histo'])=zeros(size(DataOut.(VarName)));
-                            VarMesh=DataOut.(VarName)(2)-DataOut.(VarName)(1);
-                        end
-                    end
-                    disp(['mesh for histogram = ' num2str(VarMesh)])
-                else
-                    errorvar=zeros(numel(Field.ListVarName));%index of errorflag associated to each variable
-                    if isfield(Field,'VarAttribute')
-                        for ivar=1:numel(Field.ListVarName)
-                            VarName=Field.ListVarName{ivar};
-                            DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
-                            NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
-                            
-                            for iivar=1:length(Field.VarAttribute)
-                                if isequal(Field.VarDimName{iivar},Field.VarDimName{ivar})&& isfield(Field.VarAttribute{iivar},'Role')...
-                                        && strcmp(Field.VarAttribute{iivar}.Role,'errorflag')
-                                    errorvar(ivar)=iivar; % index of the errorflag variable corresponding to ivar
-                                end
+                        DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
+                        NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
+                        
+                        for iivar=1:length(Field.VarAttribute)
+                            if isequal(Field.VarDimName{iivar},Field.VarDimName{ivar})&& isfield(Field.VarAttribute{iivar},'Role')...
+                                    && strcmp(Field.VarAttribute{iivar}.Role,'errorflag')
+                                errorvar(ivar)=iivar; % index of the errorflag variable corresponding to ivar
                             end
                         end
-                        DataOut.ListVarName(errorvar(errorvar~=0))=[]; %remove errorflag from result
-                        DataOut.VarDimName(errorvar(errorvar~=0))=[]; %remove errorflag from result
-                        DataOut.VarAttribute(errorvar(errorvar~=0))=[]; %remove errorflag from result
+                    end
+                    DataOut.ListVarName(errorvar(errorvar~=0))=[]; %remove errorflag from result
+                    DataOut.VarDimName(errorvar(errorvar~=0))=[]; %remove errorflag from result
+                    DataOut.VarAttribute(errorvar(errorvar~=0))=[]; %remove errorflag from result
+                else
+                    for ivar=1:numel(Field.ListVarName)
+                        VarName=Field.ListVarName{ivar};
+                        DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
+                        NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
+                    end
+                end
+                
+            end
+        end   %current field
+        for ivar=1:length(DataOut.ListVarName)
+            VarName=DataOut.ListVarName{ivar};
+            sizmean=size(DataOut.(VarName));
+            siz=size(Field.(VarName));
+            if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})
+                if isfield(Data{1},VarName)
+                    MaxValue=max(DataOut.(VarName));% current max of histogram absissa
+                    MinValue=min(DataOut.(VarName));% current min of histogram absissa
+                    %                     VarMesh=Field.VarAttribute{ivar}.Mesh;
+                    MaxIndex=round(MaxValue/VarMesh);
+                    MinIndex=round(MinValue/VarMesh);
+                    MaxIndex_new=round(max(Field.(VarName)/VarMesh));% max of the current field
+                    MinIndex_new=round(min(Field.(VarName)/VarMesh));
+                    if MaxIndex_new>MaxIndex% the variable max for the current field exceeds the previous one
+                        DataOut.(VarName)=[DataOut.(VarName) VarMesh*(MaxIndex+1:MaxIndex_new)];% append the new variable values
+                        DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(1,MaxIndex_new-MaxIndex)]; % append the new histo values
+                    end
+                    if MinIndex_new <= MinIndex-1
+                        DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex-1) DataOut.(VarName)];% insert the new variable values
+                        DataOut.([VarName 'Histo'])=[zeros(1,MinIndex-MinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values
+                        ind_start=1;
                     else
-                        for ivar=1:numel(Field.ListVarName)
-                            VarName=Field.ListVarName{ivar};
-                            DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
-                            NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
-                        end
-                    end
-                    
+                        ind_start=MinIndex_new-MinIndex+1;
+                    end
+                    DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)=...
+                        DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)+Field.([VarName 'Histo']);
                 end
-            end   %current field
-            for ivar=1:length(DataOut.ListVarName)
-                VarName=DataOut.ListVarName{ivar};
-                sizmean=size(DataOut.(VarName));
-                siz=size(Field.(VarName));
-                if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})
-                    if isfield(Data{1},VarName)
-                        MaxValue=max(DataOut.(VarName));% current max of histogram absissa
-                        MinValue=min(DataOut.(VarName));% current min of histogram absissa
-                        %                     VarMesh=Field.VarAttribute{ivar}.Mesh;
-                        MaxIndex=round(MaxValue/VarMesh);
-                        MinIndex=round(MinValue/VarMesh);
-                        MaxIndex_new=round(max(Field.(VarName)/VarMesh));% max of the current field
-                        MinIndex_new=round(min(Field.(VarName)/VarMesh));
-                        if MaxIndex_new>MaxIndex% the variable max for the current field exceeds the previous one
-                            DataOut.(VarName)=[DataOut.(VarName) VarMesh*(MaxIndex+1:MaxIndex_new)];% append the new variable values
-                            DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(1,MaxIndex_new-MaxIndex)]; % append the new histo values
-                        end
-                        if MinIndex_new <= MinIndex-1
-                            DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex-1) DataOut.(VarName)];% insert the new variable values
-                            DataOut.([VarName 'Histo'])=[zeros(1,MinIndex-MinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values
-                            ind_start=1;
-                        else
-                            ind_start=MinIndex_new-MinIndex+1;
-                        end
-                        DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)=...
-                            DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)+Field.([VarName 'Histo']);
-                    end
-                elseif ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
-                    disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project  on a grid'],checkrun)
-                    return
+            elseif ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
+                disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project  on a grid'],checkrun)
+                return
+            else
+                if errorvar(ivar)==0
+                    check_bad=isnan(Field.(VarName));%=0 for NaN data values, 1 else
                 else
-                    if errorvar(ivar)==0
-                        check_bad=isnan(Field.(VarName));%=0 for NaN data values, 1 else
-                    else
-                        check_bad=isnan(Field.(VarName)) | Field.(Field.ListVarName{errorvar(ivar)})~=0;%=0 for NaN or error flagged data values, 1 else
-                    end
-                    Field.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
-                    DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
-                    NbData.(VarName)=NbData.(VarName)+ ~check_bad;% records the number of data for each point
+                    check_bad=isnan(Field.(VarName)) | Field.(Field.ListVarName{errorvar(ivar)})~=0;%=0 for NaN or error flagged data values, 1 else
                 end
-            end
-            %%%%%%%%%%%%   END MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
+                Field.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
+                DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
+                NbData.(VarName)=NbData.(VarName)+ ~check_bad;% records the number of data for each point
+            end
+        end
+        %%%%%%%%%%%%   END MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
+    end
+    %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%%
+    
+    if ~(isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'}))
+        for ivar=1:length(Field.ListVarName)
+            VarName=Field.ListVarName{ivar};
+            DataOut.(VarName)=DataOut.(VarName)./NbData.(VarName); % normalize the mean
+        end
+    end
+    nbmissing=numel(index_series+index_j(islice)-index_j(1))-nbfiles;
+    if nbmissing~=0
+        if NbSlice_j==1
+        disp_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipped'],checkrun)
         else
-            disp(errormsg)
-        end
-    end
-    %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%%
-
-if ~(isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'}))
-    for ivar=1:length(Field.ListVarName)
-        VarName=Field.ListVarName{ivar};
-        DataOut.(VarName)=DataOut.(VarName)./NbData.(VarName); % normalize the mean
-    end
-end
-nbmissing=NbField-nbfiles;
-if nbmissing~=0
-    disp_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipped'],checkrun)
-end
-if isempty(time) % time is read from files
-    if isfield(Field,'Time')
-        time_end=Field.Time(1);%last time read
-        if ~isempty(time_1)
-            DataOut.Time=time_1;
-            DataOut.Time_end=time_end;
-        end
-    end
-else  % time from ImaDoc prevails if it exists
-    DataOut.Time=time(1);
-    DataOut.Time_end=time(end);
-end
-
-%% writing the result file
-OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out);
-if strcmp(FileExtOut,'.png') %case of images
-    if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16))
-        DataOut.A=uint16(DataOut.A);
-        imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images
-    else
-        DataOut.A=uint8(DataOut.A);
-        imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images
-    end
-    disp([OutputFile ' written']);
-else %case of netcdf  file , determine global attributes
-    errormsg=struct2nc(OutputFile,DataOut); %save result file
-    if isempty(errormsg)
+            disp(['WARNING: ' num2str(nbmissing) ' input files are missing or skipped in slice ' num2str(islice)])
+        end
+    end
+    if isempty(time) % time is read from files
+        if isfield(Field,'Time')
+            time_end=Field.Time(1);%last time read
+            if ~isempty(time_1)
+                DataOut.Time=time_1;
+                DataOut.Time_end=time_end;
+            end
+        end
+    else  % time from ImaDoc prevails if it exists
+        DataOut.Time=time(1);
+        DataOut.Time_end=time(end);
+    end
+    
+    %% writing the result file
+    OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out);
+    if strcmp(FileExtOut,'.png') %case of images
+        if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16))
+            DataOut.A=uint16(DataOut.A);
+            imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images
+        else
+            DataOut.A=uint8(DataOut.A);
+            imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images
+        end
         disp([OutputFile ' written']);
-    else
-        disp(['error in writting result file: ' errormsg])
-    end
-end  % end averaging  loop
+    else %case of netcdf  file , determine global attributes
+        errormsg=struct2nc(OutputFile,DataOut); %save result file
+        if isempty(errormsg)
+            disp([OutputFile ' written']);
+        else
+            disp(['error in writting result file: ' errormsg])
+        end
+    end  % end averaging  loop
 end
 

trunk/src/series/merge_proj.m

@@ -111 +111 @@
 end
 
-%% root input file type
+%% root input file(s) name, type and index series
 RootPath=Param.InputTable(:,1);
 RootFile=Param.InputTable(:,3);
@@ -117 +117 @@
 NomType=Param.InputTable(:,4);
 FileExt=Param.InputTable(:,5);
+
+hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
+% gives the series of input file names and indices set by the input parameters:
 [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
-%%%%%%%%%%%%
-% The cell array filecell is the list of input file names, while
 % filecell{iview,fileindex}:
 %        iview: line in the table corresponding to a given file series
-%        fileindex: file index within  the file series, 
+%        fileindex: file index with i and j reshaped as a 1D array
 % i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j 
 % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
-%%%%%%%%%%%%
-% NbSlice=1;%default
-% if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
-%     NbSlice=Param.IndexRange.NbSlice;
-% end
+if ~isempty(hdisp),delete(hdisp),end;%end the waiting display
+
 NbView=numel(i1_series);%number of input file series (lines in InputTable)
 NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)

trunk/src/series/time_series.m

@@ -153 +153 @@
 NomType=Param.InputTable(:,4);
 FileExt=Param.InputTable(:,5);
+
 hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
+% gives the series of input file names and indices set by the input parameters:
 [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
-if ~isempty(hdisp),delete(hdisp),end;
-%%%%%%%%%%%%
-% The cell array filecell is the list of input file names, while
 % filecell{iview,fileindex}:
 %        iview: line in the table corresponding to a given file series
-%        fileindex: file index within  the file series,
-% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j
+%        fileindex: file index with i and j reshaped as a 1D array
+% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j 
 % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
-%%%%%%%%%%%%
-nbview=numel(i1_series);%number of input file series (lines in InputTable)
-nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
-nbfield_i=size(i1_series{1},2); %nb of fields for the i index
-nbfield=nbfield_j*nbfield_i; %total number of fields
+if ~isempty(hdisp),delete(hdisp),end;%end the waiting display
+
+NbView=numel(i1_series);%number of input file series (lines in InputTable)
+NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
+NbField_i=size(i1_series{1},2); %nb of fields for the i index
+NbField=NbField_j*NbField_i; %total number of fields
 
 %% determine the file type on each line from the first input file